Alonso-Stepanova Laboratory

Publications

Selected publications:


-. Systems analysis of auxin transport in the Arabidopsis root apex. Band LR1, Wells DM, Fozard JA, Ghetiu T, French AP, Pound MP, Wilson MH, Yu L, Li W, Hijazi HI, Oh J, Pearce SP, Perez-Amador MA, Yun J, Kramer E, AlonsoJM, Godin C, Vernoux T, Hodgman TC, Pridmore TP, Swarup R, King JR, Bennett MJ. Plant Cell. 26:862-875 (2014)


-.A Recombineering-Based Gene Tagging System for Arabidopsis. Alonso JM, Stepanova AN. Methods Mol Biol. 1062:271-283 (2014)


-.Local auxin sources orient apical-basal axis in Arabidopsis embryos. Robert H.S., Grones P., Stepanova A.N., Robles L.M., Lokerse A.S., Alonso J.M., Weijers D., Friml J. Curr. Biol. 23:2506-2512 (2013)


-.Arabidopsis SABRE and CLASP interact to stabilize cell division plane orientation and planar polarity. Pietra S., Gustavsson A., Kiefer C., Kalmbach L., Hörstedt P., Ikeda Y., Stepanova A., Alonso JM, Grebe M. Nat Commu 15;4:2779 (2013)


-.Arabidopsis transformation with large bacterial artificial chromosomes. Alonso JM, Stepanova AN. Methods Mol Biol. 1062:271-83 (2014)


-.Molecular Mechanisms of Ethylene-Auxin Interactions. Robles L, Stepanova A, Alonso J. Molecular Plant. doi:10.1093/mp/sst113 (2013)


-.Genetic aspects of auxin biosynthesis and its regulation. Brumos J, Alonso JM, Stepanova AN. Physiol Plant. doi: 10.1111/ppl.12098. (2013)


-.Ethylene signaling: simple ligand, complex regulation. Merchante C, Alonso JM, Stepanova AN. Curr Opin Plant Biol. 16:554-60. (2013)


-.Kinetic analysis of Arabidopsis glucosyltransferase UGT74B1 illustrates a general mechanism by which enzymes can escape product inhibition. Kopycki J, Wieduwild E, Kohlschmidt J, Brandt W, Stepanova AN, Alonso JM, Pedras MS, Abel S, Grubb CD. Biochem. J. 450:37-46 (2013)


-.Functional characterization of type-B response regulators in the Arabidopsis cytokinin response. Hill K, Mathews DE, Kim HJ, Street IH, Wildes SL, Chiang YH, Mason MG, Alonso JM, Ecker JR, Kieber JJ, Schaller GE. Plant Physiol. 162:212-224 (2013)


-.AUX/LAX genes encode a family of auxin influx transporters that perform distinct functions during Arabidopsis development. Péret B, Swarup K, Ferguson A, Seth M, Yang Y, Dhondt S, James N, Casimiro I, Perry P, Syed A, Yang H, Reemmer J, Venison E, Howells C, Perez-Amador MA, Yun J, Alonso J, Beemster GT, Laplaze L, Murphy A, Bennett MJ, Nielsen E, Swarup R. Plant Cell. 2012 24:2874-85 (2012)


-. The Arabidopsis YUCCA1 flavin monooxygenase functions in the indole-3-pyruvic acid branch of auxin biosynthesis. Stepanova AN, Yun J, Robles LM, Novak O, He W, Guo H, Ljung K, Alonso JM. Plant Cell. 23:3961-3973 (2011)


-. A Small-Molecule Screen Identifies L-Kynurenine That Competitively Inhibits TAA1/TAR Activity in Ethylene-Directed Auxin Biosynthesis and Root Growth. He W, Brumos J, Li H, Ji Y, Ke M, Gong X, Zeng Q, Li W, Zhang X, An F, Wen X, Li P, Xie D, Stepanova A, Alonso J, and Guo H. Plant Cell. 23: 3944-3960 (2011)


-. Bypassing transcription: a shortcut in cytokinin-auxin interactions. Stepanova AN, Alonso JM. Dev. Cell. 21:608-610 (2011)


-. A recombineering-based gene tagging system for Arabidopsis. Zhou R, Benavente LM, Stepanova AN and Alonso JM. Plant J. 66:712-723 (2011).


-. Ethylene signaling and response: where different regulatory modules meet. Stepanova AN. and Alonso JM. Curr Opin Plant Biol. 12:548-55 (2009)


-. Ikeda Y, Men S, Fischer U., Stepanova AN, Alonso JM, Ljung K, and Grebe M. Local auxin biosynthesis modulates gradient-dependent planar polarity in Arabidopsis Nature Cell Biol. 11:731-738 (2009)


-. TAA1-mediated auxin biosynthesis is essential for hormone crosstalk and plant development. Stepanova AN, Robertson-Hoyt J, Yun J, Benavente LM, Xie D, Doležal K, Schlereth A, Jürgens G, and Alonso JM.  Cell. 133:177-191 (2008)

         -. An adapter ligation-mediated PCR method for high-throughput mapping of T-DNA inserts in the Arabidopsis genome. O’Malley RC, Alonso JM, Kim CJ, Leisse TJ, and & Ecker JR. Nature Protocols 2:2910-17 (2007)


-. Multilevel Interactions between Ethylene and Auxin in Arabidopsis Roots. Stepanova AN, Yun J, Likhacheva AV, Alonso JM. Plant Cell 19:2169-85 (2007)


-. Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. Alonso JM, Ecker JR. Nat. Rev. Genet. 7:524-536 (2006)


-. Molecular mechanisms of ethylene signaling in Arabidopsis. Larissa M. Benavente and Jose M. Alonso. Mol. BioSyst. 2:165-173 (2006)


        -. A Link between ethylene and auxin uncovered by the characterization of two root-specific ethylene-insensitive mutants in Arabidopsis. Stepanova AN, Hoyt JM, Hamilton AA, Alonso JM. Plant Cell. 17:2230-42 (2005)


        -. Ethylene signaling and response pathway: A unique signaling cascade with a multitude of inputs and outputs. Stepanova, A.N. and Alonso, J.M. Physiol. Plant. 123:195-206 (2005).


          -. The Ethylene Signaling Pathway. Alonso, J.M and Stepanova, A.S. Science 306:1513-1515 (2004)

       -. Convergence of signaling pathways in the control of differential cell growth in Arabidopsis.  Li H, Johnson P, Stepanova A, Alonso JM, Ecker JR. Dev. Cell 7:193-204 (2004)

-. Genome-wide insertional mutagenesis of Arabidopsis thaliana. Alonso, J.M., Stepanova, A.N., Leisse, T.J., Kim, C.J., Chen, H., Shinn, P., Stevenson, D.K., Zimmerman, J., Barajas, P., Cheuk, R., Gadrinab, C., Heller, C., Jeske, A., Koesema, E., Meyers, C.C., Parker, H., Prednis, L., Ansari, Y., Choy, N., Deen, H., Geralt, M., Hazari, N., Hom, E., Karnes, M., Mulholland, C., Ndubaku, R., Schmidt, I., Guzman, P., Aguilar-Henonin, L., Schmid, M., Weigel, D., Carter, D.E., Marchand, T., Risseeuw, E., Brogden, D., Zeko, A., Crosby, W.L., Berry , C.C., Ecker, J.R. Science 301:653-657 (2003)

-. Five components of the ethylene-response pathway identified in a screening for weak ethylene-insensitive mutants in Arabidopsis. Jose M. Alonso, Anna N. Stepanova, Roberto Solano, Ellen Wisman, Simone Ferrari, Frederick M. Ausubel and Joseph R. Ecker. PNAS 100:2992-2997 (2003).


-. "The Ethylene Pathway: A Paradigm for Plant Hormone Signaling and Interaction". Jose M. Alonso and Joseph R. Ecker. Science's STKE (2001). http://stke.sciencemag.org/cgi/content/full/sigtrans;2001/70/re1.


-. "Chromosome 1 of Arabidopsis thaliana". Theologis et al. Nature 408:816-820 (2000).

-. "EIN2, a Bifunctional Transducer of Ethylene and Stress Responses in Arabidopsis". Jose M. Alonso, Takashi Hirayama, Gregg Roman, Saeid Nourizadeh and Joseph R. Ecker. Science 284:2148-2152 (1999).

-. "RESPONSIVE-TO-ANTAGONIST1, a Menkes/Wilson Disease-Related Copper Transporter, Is Required for Ethylene Signaling in Arabidopsis". Takashi Hirayama, Joseph J. Kieber, Noriko Hirayama, Mikhail Kogan, Plinio Guzman, Saeid Nourizadeh, Jose M. Alonso, William P. Dailey, Andrew Dancis, and Joseph R. Ecker. Cell 97:383-393 (1999).



Other publications

-. "Two dimensional gel electrophoresis patterns of total, in vivo labeled and in vitro translated polypeptides from orange flavedo during maturation and following ethylene treatment". Alonso, J.M., García-Martínez, J.L., Chamarro, J. . Physiol. Plant. 85: 147-156 (1992)

-. "Evidence for the involvement of ethylene in the expression of specific RNAs during maturation of the orange, a nonclimacteric fruit" Alonso, J.M., Chamarro, J. and Granell, A. Plant Molecular Biology.29: 385-390 (1995).

-. "A putative vacuolar processing protease is regulated by ethylene and also during fruit ripening in citrus-fruit". Alonso, J.M. and Granell, A. Plant Physiology 109: 541-547 (1995)

-. "A nonphotosynthetic ferredoxin gene is induced by ethylene in citrus organs". Alonso, J.M., Chamarro, J., Granell, A. Plant Molecular Biology 29: 1211-1221 (1995)

-. "Ethylene Captured a Metal. Metal Ions are Involved in Ethylene Perception and Signal Transduction." Takashi Hirayama and Jose M. Alonso. (Review). Plant Cell Physiology 41: 548-555 (2000).

-. "Involvement of NRAMP1 from Arabidopsis thaliana in Iron Transport." Catherine Curie*, Jose M. Alonso*, Marie Le Jean, Joe Ecker and Jean-François Briat. Biochem. J. 347: 749-755 (2000). (*Authors contributed equally to this work.)


-. "An Arabidopsis Circadian Clock Component Interacts with Both CRYI and PHYB". Jarillo, J. A., Capel, J., Tang, R.-H., Yang, H.-Q., Alonso, J. M., Ecker, J. R. and Cashmore, A. R.  Nature 410: 487-490 (2001).


-. "Phototropin-Related NPL1 Controls Chloroplast Relocation Induced by Blue Light.". Jarillo, J. A., Capel, J., Gabrys, H., Alonso, J. M., Ecker, J. R. and Cashmore, A. R. Nature 410: 952-854 (2001)


-. “NPSN11 is a cell plate-associated SNARE protein that interacts with the syntaxin KNOLLE” Zheng, H. Bednarek, S. Y. Sanderfoot, A. A. Alonso, J. Ecker, J. R. and Raikhel, N. V. Plant Physiol 129: 530-539 (2002)


-. A role for peroxisomes in photomorphogenesis and development of Arabidopsis” Jianping Hu, Maria Aguirre, Charles Peto, José Alonso, Joseph Ecker, Joanne Chory. Science 297: 405-409 (2002).


-. “De-etiolated 1 (DET1) and Damaged DNA Binding Protein 1 (DDB1) Interact to Regulate Arabidopsis Photomorphogenesis” Dana F. Schroeder, Manfred Gahrtz, Bridey B. Maxwell, R. Kim Cook, Jack M. Kan, Jose M. Alonso, Joseph R. Ecker, and Joanne Chory. Current Biology 12:1462-1472 (2002).


-. Trp-dependent auxin biosynthesis in Arabidopsis: involvement of cytochrome P450s CYP79B2 and CYP79B3. Yunde Zhao, Anna K. Hull, Neeru Gupta, Kendrick A. Goss, Jose Alonso, Joseph R. Ecker, Jennifer Normanly, Joanne Chory, and John L. Celenza. Genes and Dev. 16:3100-3112 (2002)


-. Three Redundant Brassinosteroid Early Response Genes Encode Putative bHLH Transcription Factors Required for Normal Growth. Danielle Friedrichsen, Jennifer Nemhauser, Takamichi Muramitsu, Julin N. Maloof, José Alonso, Joseph R. Ecker, Masaki Furuya, Joanne Chory.. Genetics 162:1445-1456 (2002)


-. ABA-Activated SnRK2 Protein Kinase is Required for Dehydration Stress Signaling in Arabidopsis. Riichiro Yoshida, Tokunori Hobo, Kazuya Ichimura, Tsuyoshi Mizoguchi, Fuminori Takahashi, Jose Alonso, Joseph R. Ecker and Kazuo Shinozaki. Plant Cell Physiol 43: 1473-1483 (2002)



-. Mg-protoporphyrinIX is a signalling molecule involved in retrograde communication between the chloroplast and nucleus. Åsa Strand, Tadao Asami, Jose Alonso, Joseph R. Ecker, and Joanne Chory.. Nature 421:79-83 (2003)


-. The â-Subunit of the Arabidopsis G Protein Negatively Regulates Auxin-Induced Cell Division and Affects Multiple Developmental Processes. Hemayet Ullah, Jin-Gui Chen, Brenda Temple, Douglas C. Boyes, Jose M. Alonso, Keith R. Davis, Joseph R. Ecker, Alan M. Jones. Plant Cell 15:393-409 (2003)

-. GUN4, a Regulator of Chlorophyll Synthesis and Intracellular Signaling. Larkin, R.M., Alonso, J., Ecker, J., Chory, J. Science 299:902-906 (2003).


-. Arabidopsis RIN4 is a target of the Type III virulence effector AvrRpt2 and modulates RPS2-mediated resistance. Mackey, D., Belkhadir, Y., Alonso, J.M., Ecker, J.R. and Dangl, J.L. Cell. 112: 379-389 (2003).


-. Isolation and Characterization of phyC Mutants in Arabidopsis Reveals Complex Crosstalk between Phytochrome Signaling Pathways. Elena Monte, José M. Alonso, Joseph R. Ecker, Yuelin Zhang, Xin Li, Jeff Young, Sandra Austin-Phillips, and Peter H. Quail.  Plant Cell 15: 1962-1980. (2003)


-. Enhanced Fitness Conferred by Naturally Occurring Variation in the Circadian Clock. Todd P. Michael, Patrice A. Salomé, Hannah J. Yu, Taylor R. Spencer, Emily L. Sharp, Mark A. McPeek, José M. Alonso, Joseph R. Ecker, and C. Robertson McClung.  Science 7:1049-1053 (2003)


-. The Balance between phytochrome kinase substrate1 and PKS2 Provides Homeostasis for Phytochrome A Signaling in Arabidopsis.  Patricia Lariguet, Hernan E. Boccalandro, José M. Alonso, Joseph R. Ecker, Joanne Chory, Jorge J. Casal, and Christian Fankhauser. Plant Cell 15: 2966-2978. (2003)


-. Mutations in the Ca2+/H+ Transporter CAX1 Increase CBF/DREB1 Expression and the Cold-Acclimation Response in Arabidopsis. Rafael Catalá, Elisa Santos, José M. Alonso, Joseph R. Ecker, José M. Martínez-Zapater, Julio Salinas. Plant Cell 15: 2940-2951 (2003)

-. Type-A ARRs are Partially Redundant Negative Regulators of Cytokinin Signaling in Arabidopsis. Jennifer P.C. To, Georg Haberer, Fernando J. Ferreira, Jean Deruere, Michael G. Mason, G. Eric Schaller, Jose M. Alonso, Joseph R. Ecker, and Joseph J. Kieber. Plant Cell 16: 658-671 (2004)

-. CBF2/DREB1C is a negative regulator of CBF1/DREB1B and CBF3/DREB1A expression and plays a central role in stress tolerance in Arabidopsis. Fernando Novillo, Jose M. Alonso, Joseph R. Ecker and Julio Salinas. PNAS 101: 3985-3990 (2004)

-. Flagellin is not a major defense elicitor in Ralstonia solanacearum cells or extracts applied to Arabidopsis thaliana. Pfund C, Tans-Kersten J, Dunning FM, Alonso JM, Ecker JR, Allen C, Bent AF. Mol Plant Microbe Interact. 17:696-706 (2004)

-. GCR1 Can Act Independently of Heterotrimeric G-Protein in Response to Brassinosteroids and Gibberellins in Arabidopsis Seed Germination. Chen JG, Pandey S, Huang J, Alonso JM, Ecker JR, Assmann SM, Jones AM. Plant Physiol. 135: 907-915 (2004)

-. Della proteins and gibberellin-regulated seed germination and floral development in Arabidopsis. Tyler L, Thomas SG, Hu J, Dill A, Alonso JM, Ecker JR, Sun TP. Plant Physiol. 135:1008-1019 (2004)

-. A homolog of prokaryotic thiol-disulfide transporter CcdA is required for the assembly of the cytochrome b6f complex in Arabidopsis chloroplasts. Page ML, Hamel PP, Gabilly ST, Zegzouti H, Perea JV, Alonso JM, Ecker JR, Theg SM, Christensen SK, Merchant S. J Biol Chem.   279: 32474-32482  (2004)


-. The phytochrome-interacting transcription factor, PIF3, acts early, selectively, and positively in light-induced chloroplast development. Monte E, Tepperman JM, Al-Sady B, Kaczorowski KA, Alonso JM, Ecker JR, Li X, Zhang Y, Quail PH. Proc Natl Acad Sci US 101:16091-16098 (2004).


-. Regulation of flowering time in Arabidopsis by K homology domain proteins. Mockler TC, Yu X, Shalitin D, Parikh D, Michael TP, Liou J, Huang J, Smith Z, Alonso JM, Ecker JR, Chory J, Lin C. Proc Natl Acad Sci US 101: 12759-12764 (2004)


-. Ethylene signaling pathway. Stepanova AN, Alonso JM. Sci STKE: 2005(276):cm3 (2005).


-. Arabidopsis ethylene signaling pathway. Stepanova AN, Alonso JM. Sci STKE: 2005(276):cm3 (2005).


-. Phytochrome-specific type 5 phosphatase controls light signal flux by enhancing phytochrome stability and affinity for a signal transducer. Ryu JS, Kim JI, Kunkel T, Kim BC, Cho DS, Hong SH, Kim SH, Fernandez AP, Kim Y, Alonso JM, Ecker JR, Nagy F, Lim PO, Song PS, Schafer E, Nam HG. Cell: 120:395-406 (2005)

-. Functional Genomic Analysis of the AUXIN RESPONSE FACTOR Gene Family Members in Arabidopsis thaliana: Unique and Overlapping Functions of ARF7 and ARF19. Okushima Y, Overvoorde PJ, Arima K, Alonso JM, Chan A, Chang C, Ecker JR, Hughes B, Lui A, Nguyen D, Onodera C, Quach H, Smith A, Yu G, Theologis A. Plant Cell. 17:444-463. (2005)


-. An Arabidopsis NPR1-like gene, NPR4, is required for disease resistance. Liu G, Holub EB, Alonso JM, Ecker JR, Fobert PR. Plant J. 41: 304-18 (2005).


-. Class III Homeodomain-Leucine Zipper Gene Family Members Have Overlapping, Antagonistic, and Distinct Roles in Arabidopsis Development. Prigge MJ, Otsuga D, Alonso JM, Ecker JR, Drews GN, Clark SE. Plant Cell. 17:61-76 (2005)


-. A Link between ethylene and auxin uncovered by the characterization of two root-specific ethylene-insensitive mutants in Arabidopsis. Stepanova AN, Hoyt JM, Hamilton AA, Alonso JM. Plant Cell. 17:2230-42 (2005)


-. NPH4/ARF7 and ARF19 promote leaf expansion and auxin-induced lateral root formation. Wilmoth JC, Wang S, Tiwari SB, Joshi AD, Hagen G, Guilfoyle TJ, Alonso JM, Ecker JR, Reed JW. Plant J. 43:118-30 (2005).


-. Auxin response factors ARF6 and ARF8 promote jasmonic acid production and flower maturation. Nagpal P, Ellis CM, Weber H, Ploense SE, Barkawi LS, Guilfoyle TJ, Hagen G, Alonso JM, Cohen JD, Farmer EE, Ecker JR, Reed JW. Development. 132:4107-18 (2005)


-. Functional Genomic Analysis of the AUXIN/INDOLE-3-ACETIC ACID Gene Family Members in Arabidopsis thaliana. Overvoorde PJ, Okushima Y, Alonso JM, Chan A, Chang C, Ecker JR, Hughes B, Liu A, Onodera C, Quach H, Smith A, Yu G, Theologis A. Plant Cell. 17:3282-300 (2005)


-. Multiple type-B response regulators mediate cytokinin signal transduction in Arabidopsis. Mason MG, Ma. thews DE, Argyros DA, Maxwell BB, Kieber JJ, Alonso JM, Ecker JR, Schaller GE. Plant Cell. 17:3007-18 (2005).


-. Downregulation of ClpR2 Leads to Reduced Accumulation of the ClpPRS Protease Complex and Defects in Chloroplast Biogenesis in Arabidopsis. Rudella A, Friso G, Alonso JM, Ecker JR, van Wijk KJ. Plant Cell. 18: 1704-1721 (2006)


-. RACK1 mediates multiple hormone responsiveness and developmental processes in Arabidopsis. Chen JG, Ullah H, Temple B, Liang J, Guo J, Alonso JM, Ecker JR, Jones AM. J Exp Bot. 57: 2697-2708 (2006)


-. PHYTOCHROME KINASE SUBSTRATE 1 is a phototropin 1 binding protein required for phototropism. Lariguet P, Schepens I, Hodgson D, Pedmale UV, Trevisan M, Kami C, de Carbonnel M, Alonso JM, Ecker JR, Liscum E, Fankhauser C. Proc Natl Acad Sci U S A. 2006 103(26):10134-9 (2006)


-. CDPKs CPK6 and CPK3 Function in ABA Regulation of Guard Cell S-Type Anion- and Ca(2+)- Permeable Channels and Stomatal Closure. Mori IC, Murata Y, Yang Y, Munemasa S, Wang YF, Andreoli S, Tiriac H, Alonso JM, Harper JF, Ecker JR, Kwak JM, Schroeder JI. PLoS Biol. 4: 1749-1762 (2006)


-. Localization of Iron in Arabidopsis Seed Requires the Vacuolar Membrane Transporter VIT1. Sun A. Kim, Tracy Punshon, Antonio Lanzirotti, Liangtao Li, José M. Alonso, Joseph R. Ecker, Jerry Kaplan, and Mary Lou Guerinot. Science 314:1295-1298 (2006)


-. The Arabidopsis Histidine Phosphotransfer Proteins Are Redundant Positive Regulators of Cytokinin Signaling. Hutchison CE, Li J, Argueso C, Gonzalez M, Lee E, Lewis MW, Maxwell BB, Perdue TD, Schaller GE, Alonso JM, Ecker JR, Kieber JJ. Plant Cell. 18:3073-87 (2006)


-. A WD40 Domain Cyclophilin Interacts with Histone H3 and Functions in Gene Repression and Organogenesis in Arabidopsis. Li H, He Z, Lu G, Lee SC, Alonso J, Ecker JR, Luan S. Plant Cell. 19:2403-16 (2007)


-. Genome-Wide High-Resolution Mapping of Exosome Substrates Reveals Hidden Features in the Arabidopsis Transcriptome. Chekanova JA, Gregory BD, Reverdatto SV, Chen H, Kumar R, Hooker T, Yazaki J, Li P, Skiba N, Peng Q, Alonso J, Brukhin V, Grossniklaus U, Ecker JR, Belostotsky DA. Cell 131:1340-1353 (2007)


-. The Arabidopsis Phytochrome-Interacting Factor PIF7, Together with PIF3 and PIF4, Regulates Responses to Prolonged Red Light by Modulating phyB Levels. Leivar P, Monte E, Al-Sady B, Carle C, Storer A, Alonso JM, Ecker JR, Quail PH. Plant Cell 20:337-352 (2008)


-. Potential sites of bioactive gibberellin production during reproductive growth in Arabidopsis. Hu J, Mitchum MG, Barnaby N, Ayele BT, Ogawa M, Nam E, Lai WC, Hanada A, Alonso JM, Ecker JR, Swain SM, Yamaguchi S, Kamiya Y, Sun TP. Plant Cell 20:320-336 (2008)


-. A Combinatorial Interplay Among the 1-Aminocyclopropane-1-carboxylate Isoforms Regulates Ethylene Biosynthesis in Arabidopsis thaliana. Tsuchisaka A, Yu G, Jin H, Alonso JM, Ecker JR, Zhang X, Gao S, Theologis A. Genetics. 183:979-1003 (2009)


























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